It is important to investigate whether genetic susceptible variants exercise the same effects in populations that are differentially exposed to environmental risk factors. Here, we assess the power of four two-phase case-control design strategies for assessing multiplicative gene-environment (G-E) interactions or for assessing genetic or environmental effects in the presence of G-E interactions. With a di-allelic SNP and a binary E, we obtained closed-form maximum likelihood estimates of both main effect and interaction odds ratio parameters under the constraints of G-E independence and Hardy-Weinberg Equilibrium, and used the Wald statistic for all tests. We concluded that i) for testing G-E interactions or genetic effects in the presence of G-E interactions when data for E is fully available, it is preferable to ascertain data for G in a subsample of cases with similar numbers of exposed and unexposed and a random subsample of controls; and ii) for testing G-E interactions or environmental effects in the presence of G-E interactions when data for G is fully available, it is preferable to ascertain data for E in a subsample of cases that has similar numbers for each genotype and a random subsample of controls. In addition, supplementing external control data to an existing casecontrol sample leads to improved power for assessing effects of G or E in the presence of G-E interactions.
Gene-environment interaction; Gene-environment independence; Hardy-Weinberg equilibrium; Retrospective maximum likelihood; Two-phase design
Cancer causes significant symptom burden and diminished quality of life. Despite the expansion of supportive and palliative care services (SPCS), little is known about rates of utilization and barriers to access to these services among oncology outpatients.
We performed a cross-sectional survey in three outpatient medical oncology clinics. Patients with a diagnosis of breast, lung, or gastrointestinal (GI) cancer and a Karnofsky score of ≥60 were included. Patients reported their use of SPCS and any perceived barriers. Multivariable logistic regression was used to identify factors associated with SPCS use.
Among 313 participants, (50.5%) had not used SPCS since cancer diagnosis. The most common services used were nutrition (26.5%), psychiatric/psychological counseling (29.7%), and physical therapy (15.1%). Pain/palliative care and cancer rehabilitation consultations were used by 8.5% and 4.1% of participants, respectively. In multivariate analysis, graduate education was associated with greater SPCS use (adjusted odds ratio [AOR] 2.14, 95% confidence interval [CI] 1.08-4.26) compared with those with high school or less, whereas having lung cancer was associated with less SPCS use (AOR 0.48, 95% CI 0.24-0.96) when compared with those having breast cancer. The biggest reported barriers to using SPCS were a lack of awareness (22.4%) and lack of physician referral (23%).
Approximately half of these patients had not accessed SPCS since cancer diagnosis and cite lack of awareness and physician nonreferral as barriers. Further research is needed to understand patients' needs and beliefs regarding SPCS, and how to integrate SPCS into conventional treatments to improve cancer care.
Next-generation sequencing technology provides an unprecedented opportunity to identify rare susceptibility variants. It is not yet financially feasible to perform whole-genome sequencing on a large number of subjects, and a two-stage design has been advocated to be a practical option. In stage I, variants are discovered by sequencing the whole genomes of a small number of carefully selected individuals. In stage II, the discovered variants of a large number of individuals are genotyped to assess association. Individuals with extreme phenotypes are typically selected in stage I. Using simulated data for unrelated individuals, we explore two important aspects of this two-stage design: the efficiency of discovering common and rare single-nucleotide polymorphisms (SNPs) in stage I and the impact of incomplete SNP discovery in stage I on the power of testing associations in stage II. We apply a sum test and a sum of squared score test for gene-based association analyses evaluating the power of the two-stage design. We obtained the following results from extensive simulation studies and analysis of the GAW17 dataset. When individuals with trait values more extreme than the 99.7 to 99th quantile are included in stage I, the two-stage design could achieve the same as or even higher power than one-stage design if the rare causal variants have large effect sizes. In such tests, fewer than half of the total SNPs including more than half of the causal SNPs were discovered, which included nearly all SNPs with minor allele frequencies (MAFs) ≥ 5%, more than half of the SNPs with MAFs between 1% and 5%, and fewer than half of the SNPs with MAFs <1%. Although a one-stage design may be preferable to identify multiple rare variants having small to moderate effect sizes, our observations support using the two-stage design as a cost-effective option for next-generation sequencing studies.
Two-stage design; Next-generation sequencing; SNP discovery; Rare variants
Recent studies suggest that polymorphisms in genes encoding enzymes involved in drug detoxification and metabolism may influence disease outcome in pediatric acute lymphoblastic leukemia (ALL). We sought to extend current knowledge by using standard and novel statistical methodology to examine polymorphic variants of genes and relapse risk, toxicity, and drug dose delivery in standard risk ALL.
We genotyped and abstracted chemotherapy drug dose data from treatment roadmaps on 557 patients on the Children’s Cancer Group ALL study, CCG-1891. Fourteen common polymorphisms in genes involved in folate metabolism and/or phase I and II drug detoxification were evaluated individually and clique-finding methodology was employed for detection of significant gene-gene interactions.
After controlling for known risk factors, polymorphisms in four genes: GSTP1*B (HR=1.94, p=0.047), MTHFR (HR=1.61, p=0.034), MTRR (HR=1.95, p=0.01), and TS (3R/4R, HR=3.69, p=0.007), were found to significantly increase relapse risk. One gene-gene pair, MTRR A/G and GSTM1 null genotype, significantly increased the risk of relapse after correction for multiple comparisons (p=0.012). Multiple polymorphisms were associated with various toxicities and there was no significant difference in dose of chemotherapy delivered by genotypes.
These data suggest that various polymorphisms play a role in relapse risk and toxicity during childhood ALL therapy and that genotype does not play a role in adjustment of drug dose administered. Additionally, gene-gene interactions may increase the risk of relapse in childhood ALL and the clique method may have utility in further exploring these interactions. childhood ALL therapy.
genotype; acute lymphoblastic leukemia; prognosis; toxicity; gene-gene interactions
Acute rejection (AR) is associated with worse renal allograft outcomes. Therefore, this study investigated single nucleotide polymorphisms (SNPs) to identify genetic variants associated with AR, accounting for center variation, in a multi-center, prospective, observation study.
We enrolled patients from 6 transplant centers, 5 in the U.S. and one in Canada. A total of 2,724 SNPs were genotyped. We accounted for center variation in AR rates by stratifying by transplant center and using novel knowledge discovery methods.
There was significant center variation in AR rates across the six transplant sites. (p<0.0001) Accounting for this difference and clinical factors independently associated with AR, we identified 15 novel SNPs associated with AR with stratification by transplant center (p<0.05). We also identified 15 novel SNPs associated with severity of tubulitis scores, after adjusting for transplant center and other clinical factors independently associated with severity of tubulitis. (p<0.05) There was some overlap with one SNP associated with AR and also associated with severity of tubulitis, among the top 15 SNPs.
Center-to-center variation is a major challenge to genomic studies focused on AR. The SNPs associated with AR and severity of tubulitis in this study, will need to be validated in independent cohort of kidney transplant recipients.
single nucleotide polyrmorphisms; acute rejection; tubulitis
We consider the problem of high-dimensional regression under non-constant error variances. Despite being a common phenomenon in biological applications, heteroscedasticity has, so far, been largely ignored in high-dimensional analysis of genomic data sets. We propose a new methodology that allows non-constant error variances for high-dimensional estimation and model selection. Our method incorporates heteroscedasticity by simultaneously modeling both the mean and variance components via a novel doubly regularized approach. Extensive Monte Carlo simulations indicate that our proposed procedure can result in better estimation and variable selection than existing methods when heteroscedasticity arises from the presence of predictors explaining error variances and outliers. Further, we demonstrate the presence of heteroscedasticity in and apply our method to an expression quantitative trait loci (eQTLs) study of 112 yeast segregants. The new procedure can automatically account for heteroscedasticity in identifying the eQTLs that are associated with gene expression variations and lead to smaller prediction errors. These results demonstrate the importance of considering heteroscedasticity in eQTL data analysis.
Generalized least squares; Heteroscedasticity; Large p small n; Model selection; Sparse regression; Variance estimation
Adenosine (Ade) is an antiepileptic agent. In order to investigate the possible mechanism of action of Ade, its effect on calcium (Ca2+) oscillations in hippocampal neurons of Sprague Dawley (SD) rats was explored. Primary hippocampal neurons were cultured from suckling neonatal SD rats. Cells were cultured for 7–9 days and the Ca2+ oscillations in response to perfusion with Ade were detected using confocal laser scanning microscopy in combination with Fluo-3/AM labeling. This study found that Ade inhibits the spontaneous synchronized Ca2+ oscillation frequency and amplitude in mature hippocampal neurons and such inhibition depends on the Ade dosage level to a certain extent. Ade also had a significant inhibitory effect on high potassium-induced Ca2+ oscillation frequency and amplitude. Ade had a significant inhibitory effect on high-voltage-activated Ca2+ channel-mediated Ca2+ influx and Ca2+ oscillations in neurons. This may be one of the mechanisms for Ade to exert antiepileptic effects as an endogenous substance.
adenosine; confocal laser scanning microscope; calcium oscillation
Mannan-binding lectin (MBL), a lectin homologous to C1q, greatly facilitates C3/C4-mediated opsonophagocytosis of Candida albicans (C. albicans) by human neutrophils, and has the capacity to bind to CR1 (CD35) expressed on circulating neutrophils. The intracellular pool of neutrophil Dectin-1 plays a critical role in stimulating the reactive oxygen species (ROS) generation through recognition of β-1,3-glucan component of phagocytized zymosan or yeasts. However, little is known about whether MBL can mediate the opsonophagocytosis of Candida albicans by neutrophils independent of complement activation, and whether MBL-mediated opsonophagocytosis influence the intracellular expression of Dectin-1 and ROS production. Here we showed that the inhibited phagocytic efficiency of neutrophils as a result of blockage of Dectin-1 was compensated by exogenous MBL alone in a dose-dependent manner. Furthermore, the expressions of Dectin-1 at mRNA and intracellular protein levels were significantly up-regulated in neutrophils stimulated by MBL-pre-incubated C. albicans, while the expression of surface Dectin-1 remained almost unchanged. Nevertheless, the stimulated ROS production in neutrophils was partly and irreversibly inhibited by blockage of Dectin-1 in the presence of exogenous MBL. Confocal microscopy examination showed that intracellular Dectin-1 was recruited and co-distributed with ROS on the surface of some phagocytized yeasts. The β-1,3-glucanase digestion test further suggested that the specific recognition and binding site of human Dectin-1 is just the β-1,3-glucan moiety on the cell wall of C. albicans. These data demonstrate that MBL has an ability to mediate the opsonophagocytosis of Candida albicans by human neutrophils independent of complement activation, which is coupled with intracellular Dectin-1-triggered ROS production.
To estimate whether African ancestry, specific gene polymorphisms, and gene-environment interactions could account for some of the unexplained preterm birth variance within blacks.
We genotyped 1,509 African ancestry informative markers, cytochrome P-450 1A1 (CYP1A1) and glutathione S-transferases Theta 1 (GSTT1) variants in 1,030 self-reported black mothers. We estimated the African ancestral proportion using the ancestry informative markers for all 1,030 self-reported black mothers. We examined the effect of African ancestry and CYP1A1 and GSTT1 smoking interactions on preterm birth cases as a whole and within its subgroups: very preterm birth (gestational age less than 34 weeks); and late preterm birth (gestational age greater than 34 and less than 37 weeks). We applied logistic regression and receiver operating characteristic (ROC) curve analysis, separately, to evaluate if African ancestry and CYP1A1- and GSTT1-smoking interactions could make additional contributions to preterm birth beyond epidemiological factors.
We found significant associations of African ancestry with preterm birth (22% vs. 31%, OR=1.11; 95%CI: 1.02–1.20) and very preterm birth (23% vs. 33%, OR=1.17; 95%CI: 1.03–1.33), but not with late preterm birth (22% vs. 29%, OR=1.06; 95%CI: 0.97–1.16). In addition, the ROC curve analysis suggested that African ancestry and CYP1A1- and GSTT1-smoking interactions made substantial contributions to very preterm birth beyond epidemiologic factors.
Our data underscore the importance of simultaneously considering epidemiological factors, African ancestry, specific gene polymorphisms and gene-environment interactions to better understand preterm birth racial disparity and to improve our ability to predict preterm birth, especially very preterm birth.
For analysis of case-control genetic association studies, it has recently been shown that gene-environment independence in the population can be leveraged to increase efficiency for estimating gene-environment interaction effects in comparison with the standard prospective analysis. However, for the special case in which data on the binary phenotype and genetic and environmental risk factors can be summarized in a 2 × 2 × 2 table, the authors show here that there is no efficiency gain for estimating interaction effects, nor is there an efficiency gain for estimating the genetic and environmental main effects. This contrasts with the well-known result assuming that rare phenotype prevalence and gene-environment independence in the control population for the same data can lead to efficiency gain. This discrepancy is counterintuitive, since the 2 likelihoods are also approximately equal when the phenotype is rare. An explanation for the paradox based on a theoretical analysis is provided. Implications of these results for data analyses are also examined, and practical guidance on analyzing such case-control studies is offered.
case-control studies; epidemiologic methods; logistic models; odds ratio; prospective sampling; rare diseases; retrospective sampling
Recently meta analysis has been widely utilized to combine information across multiple studies to evaluate a common effect. Integrating data from similar studies is particularly useful in genomic studies where the individual study sample sizes are not large relative to the number of parameters of interest. In this paper, we are interested in developing robust prognostic rules for the prediction of t-year survival based on multiple studies. We propose to construct a composite score for prediction by fitting a stratified semiparametric transformation model that allows the studies to have related but not identical outcomes. To evaluate the accuracy of the resulting score, we provide point and interval estimators for the commonly used accuracy measures including the time-specific ROC curves, and positive and negative predictive values. We apply the proposed procedures to develop prognostic rules for the 5-year survival of breast cancer patients based on five breast cancer genomic studies.
Biomarker; Classification; Conditional Kaplan-Meier; Meta Analysis; Nonparametric Maximum Likelihood; Predictive Values; Prognosis; ROC; Survival Analysis
Population-based case-control design has become one of the most popular approaches for conducting genome-wide association scans for rare diseases like cancer. In this article, we propose a novel method for improving the power of the widely used single-SNP two degrees-of-freedom (2 d.f.) association test for case-control studies by exploiting the common assumption of Hardy-Weinberg Equilibrium (HWE) for the underlying population. A key feature of the method is that it can relax the assumed model constraints via a completely data-adaptive shrinkage estimation approach so that the number of false positive results due to the departure of HWE is controlled. The method is computationally simple and is easily scalable to association tests involving hundreds of thousands or millions of genetic markers. Simulation studies as well as an application involving data from a real genome-wide association study illustrate that the proposed method is very robust for large-scale association studies and can improve the power for detecting susceptibility SNPs with recessive effects, when compared to existing methods. Implications of the general estimation strategy beyond the simple 2 d.f. association test are discussed.
association test; case-control studies; genome scan; Hardy-Weinberg equilibrium; retrospective likelihood
Previous studies have shown a positive association between chronic typhoid carriage and biliary cancers. We compared serum Salmonella enterica serovar Typhi antibody titers between biliary tract cancer cases, biliary stone cases without evidence of cancer, and healthy subjects in a large population-based case-control study in Shanghai, China.
Participants included 627 newly diagnosed primary biliary tract cancer patients; 1,037 biliary stone cases (774 gallbladder and 263 bile-duct) and 959 healthy subjects without a history of cancer, randomly selected from the Shanghai Resident Registry.
Overall only 6/2,293 (0.26%) were Typhi positive. The prevalence of Typhi was 1/457 (0.22%), 4/977 (0.41%), and 1/859 (0.12%) among cancer cases, biliary-stone cases, and population controls, respectively.
We did not find an association between Typhi and biliary cancer in Shanghai, due to the very low prevalence of chronic carriers in this population.
The low seroprevalence of S. Typhi in Shanghai is unlikely to explain the high incidence of biliary cancers in this population.
Biliary tract cancer encompasses tumors of the gallbladder, bile duct and ampulla of Vater. Gallbladder cancer is more common in women, whereas bile duct cancer is more common in men, suggesting that sex hormones may play a role in the etiology of these cancers. The intracellular action of estrogens is regulated by the estrogen receptor (ESR); thus, we examined the role of common genetic variants in ESR genes on the risk of biliary tract cancers and stones in a population-based case–control study in Shanghai, China (411 cancer cases, 895 stone cases and 786 controls). We genotyped six single-nucleotide polymorphisms (SNPs), four in ESR1 (rs2234693, rs3841686, rs2228480 and rs1801132) and two in ESR2 (rs1256049 and rs4986938). In all participants, the ESR1 rs1801132 (P325P) G allele was associated with excess risks of bile duct [odds ratio (OR) = 1.7, 95% confidence interval (CI) 1.1–2.8] and ampulla of Vater cancers (OR = 2.1, 95% CI 0.9–4.9) compared with the CC genotype. The association with bile duct cancer was apparent among men (OR = 2.8, 95% CI 1.4–5.7) but not among women (P-heterogeneity = 0.01). Also, the ESR2 rs4986938 (38 bp 3′ of STP) GG genotype was associated with a higher risk of bile duct cancer (OR = 3.3, 95% CI 1.3–8.7) compared with the AA genotype, although this estimate was based on a small number of subjects. None of the other SNPs examined was associated with biliary tract cancers or stones. False discovery rate-adjusted P-values were not significant (P > 0.1). No association was found for ESR1 haplotype based on four SNPs. These preliminary results suggest that variants in ESR genes could play a role in the etiology of biliary tract cancers, especially bile duct cancer in men.
In case-control research where there are multiple case groups, standard analyses fail to make use of all available information. Multiple events case-control (MECC) studies provide a new approach to sampling from a cohort and are useful when it is desired to study multiple types of events in the cohort. In this design, subjects in the cohort who develop any event of interest are sampled, as well as a fraction of the remaining subjects. We show that a simple case-control analysis of data arising from MECC studies is biased and develop three general estimating-equation based approaches to analyzing data from these studies. We conduct simulation studies to compare the efficiency of the various MECC analyses with each other and with the corresponding conventional analyses. It is shown that the gain in efficiency by using the new design is substantial in many situations. We demonstrate the application of our approach to a nested case-control study of the effect of oral sodium phosphate use on chronic kidney injury with multiple case definitions.
Multiple events case-control study; case-cohort study; nested case-control study; sampling from a cohort; semi-parametric efficient estimator
Biliary tract cancers, encompassing the gallbladder, extrahepatic bile duct, and ampulla of Vater, are uncommon, yet highly fatal malignancies. Gallstones, the primary risk factor for biliary cancers, are linked with hyperlipidemia. We examined the associations of 12 single nucleotide polymorphisms (SNPs) of five genes in the lipid metabolism pathway with the risks of biliary cancers and stones in a population-based case-control study in Shanghai, China. We included 235 gallbladder, 125 extrahepatic bile duct, and 46 ampulla of Vater cancer cases, 880 biliary stone cases, and 779 population controls. Subjects completed an in-person interview and gave blood. Genotyping was conducted by Taqman assay using DNA from buffy coats. The effects of APOE IVS1+69 (rs440446) and APOB IVS6+360C>T (rs520354) markers were limited to men. Men carrying the G allele of APOE IVS1+69 had a 1.7-fold risk of stones (95% confidence interval (CI) =1.2–2.4), a 1.8–fold risk of gallbladder cancer (95% CI=1.0–3.3), a 3.7–fold risk of bile duct cancer (95% CI=2.0–7.0), and a 4-fold risk of ampullary cancer (95% CI=1.4–12.4). Male carriers of the T allele of APOB IVS6+360C>T had a 2-fold risk of bile duct cancer (95% CI=1.2–3.4). The APOB T-T haplotype (APOB IVS6+360C>T, EX4+56C>T) was associated with a 1.6-fold risk of bile duct cancer (95% CI=1.1–2.3). Male and female carriers of the T allele of LDLR IVS9-30C>T (rs1003723) had 1.5-fold risks of bile duct cancer. Our findings suggest that gene variants in the lipid metabolism pathway contribute to the risk of biliary tract stones and cancers, particularly of the bile duct.
single nucleotide polymorphisms; lipid metabolism; gallstones; biliary tract cancer
Cancers of the biliary tract arise from the gallbladder, extrahepatic bile ducts, and ampulla of Vater. Although relatively uncommon, the incidence of biliary tract cancer rose more than 100% in Shanghai, China between 1972 and 1994. Gallstones are the predominant risk factor for biliary tract cancers, with over 60% of the cancer cases having gallstones. Familial tendency to gallstones has been reported and may further elevate the risk of gallbladder cancer. As part of a large population-based case-control study of biliary tract cancers in Shanghai, China, we examined the association between family history of gallstones and biliary tract cancers as well as biliary stones.
A total of 627 biliary tract cancers (368 gallbladder, 191 bile duct, 68 ampulla of Vater), 1,037 biliary stone cases (774 gallbladder, 263 bile duct), and 959 healthy subjects randomly selected from the population were included in this study. Information on family history of gallstones among first-degree relatives (i.e. parents, siblings, offspring) was obtained through a self-reported history during in-person interviews.
A family history of gallstones was associated with increased risks of biliary stones (odds ratio (OR) =2.8, 95% confidence interval (CI) =2.1-3.8), gallbladder cancer (OR=2.1, 95% CI=1.4-3.3), and bile duct cancer (OR=1.5, 95% CI=0.9-2.5), after adjusting for age, gender, marital status, education, smoking, alcohol drinking, and body mass index. For gallbladder cancer, subjects with gallstones but without a family history of gallstones had a 21-fold risk (95% CI 14.8-30.1), while those with both gallstones and a positive family history had a 57-fold risk (95% CI 32.0-110.5). Significant risks for gallbladder cancer persisted after additional adjustment for gallstones, and when the analysis was restricted to subjects with first-degree relatives whose gallstones were treated with cholecystectomy. The significant associations with a family history of gallstones were seen for all first-degree relatives, including parents, siblings, and offspring, but not spouses.
This large population-based study not only supports the role of gallstones in biliary carcinogenesis but also suggests that the underlying genetic or lifestyle determinants of stones within families contribute to the risk of biliary tract cancer.
biliary tract cancer; cholelithiasis; familial aggregation; genetic susceptibility; China
We examined the associations between 21 single nucleotide polymorphisms (SNPs) of eight lipid metabolism genes and lipid levels in a Chinese population.
This study was conducted as part of a population-based study in China with 799 randomly selected healthy residents who provided fasting blood and an in-person interview. Associations between variants and mean lipid levels were examined using a test of trend and least squares mean test in a general linear model.
Four SNPs were associated with lipid levels: LDLR rs1003723 was associated with total cholesterol (p-trend=0.002) and LDL (p-trend=0.01), LDLR rs6413503 was associated with total cholesterol (p-trend=0.05), APOB rs1367117 was associated with apoB (p-trend=0.02), and ABCB11 rs49550 was associated with total cholesterol (p-trend=0.01), triglycerides (p-trend=0.01), and apoA (p-trend=0.01). We found statistically significant effects on lipid levels for LDLR rs6413503 among those with high dairy intake, LPL rs263 among those with high allium vegetable intake, and APOE rs440446 among those with high red meat intake.
We identified new associations between SNPs and lipid levels in Chinese previously found in Caucasians. These findings provide insight into the role of lipid metabolism genes, as well as the mechanisms by which these genes may be linked with disease.
single nucleotide polymorphisms; Chinese; serum lipid levels
In the genetic study of complex traits, especially behavior related ones, such as smoking and alcoholism, usually several phenotypic measurements are obtained for the description of the complex trait, but no single measurement can quantify fully the complicated characteristics of the symptom because of our lack of understanding of the underlying etiology. If those phenotypes share a common genetic mechanism, rather than studying each individual phenotype separately, it is more advantageous to analyze them jointly as a multivariate trait in order to enhance the power to identify associated genes. We propose a multilocus association test for the study of multivariate traits. The test is derived from a partially linear tree-based regression model for multiple outcomes. This novel tree-based model provides a formal statistical testing framework for the evaluation of the association between a multivariate outcome and a set of candidate predictors, such as markers within a gene or pathway, while accommodating adjustment for other covariates. Through simulation studies we show that the proposed method has an acceptable type I error rate and improved power over the univariate outcome analysis, which studies each component of the complex trait separately with multiple-comparison adjustment. A candidate gene association study of multiple smoking-related phenotypes is used to demonstrate the application and advantages of this new method. The proposed method is general enough to be used for the assessment of the joint effect of a set of multiple risk factors on a multivariate outcome in other biomedical research settings.
Generalized estimating equation; Genetic association study; Model selection; Multiple-comparison adjustment; Tree-based model
To evaluate the role of chronic inflammation in the development of gallstones and biliary tract cancer, we examined the risk associated with 62 single nucleotide polymorphisms (SNPs), including 22 inflammation-related genes, based on a population-based case-control study conducted in Shanghai, China, where the incidence of biliary tract cancer has been increasing in recent decades. The study included 411 cases with biliary tract cancer (237 gallbladder, 127 extrahepatic bile duct, and 47 ampulla of Vater), 895 with biliary stones, and 786 controls randomly selected from the population. Unconditional logistic regression was used to calculate odds ratios (ORs) and 95% confidence intervals (CIs) for the association of individual single nucleotide polymorphisms (SNPs) and haplotypes with biliary stones and biliary tract cancer. Of the 62 SNPs examined, 14 were related to the risk of biliary cancer and stones. Specifically, variants in the IL8, IL8RB, RNASEL, and NOS2 genes were associated with biliary stones, while VEGF variants were associated with gallbladder cancer. Of the 10 genes with multiple SNPs from which we inferred haplotypes, only one IL8RB haplotype, consisting of 3 SNPs (rs2230054, rs1126579, rs1126580), was associated with the risk of bile duct cancer (p=0.003) and biliary stones (p=0.02), relative to the most frequent haplotype. In summary, common variants in genes that influence inflammatory responses may predispose to gallstones and biliary tract cancer, suggesting the need for future studies into the immunologic and inflammatory pathways that contribute to biliary diseases, including cancer.
gallstones; biliary tract cancer; inflammation; genetic susceptibility
Biliary tract cancers, encompassing the gallbladder, extrahepatic bile ducts, and ampulla of Vater, are rare, but highly fatal malignancies. Gallstones, the predominant risk factor for biliary cancers, are linked with hyperlipidemia. As part of a population-based case-control study conducted in Shanghai, China, we examined the associations of serum lipid levels with biliary stones and cancers. We included 460 biliary cancer cases (264 gallbladder, 141 extrahepatic bile duct, and 55 ampulla of Vater), 981 biliary stone cases, and 858 healthy individuals randomly selected from the population. Participants completed an in-person interview and gave overnight fasting blood samples. Participants in the highest quintile of triglycerides (≥ 160 mg/dl) had a 1.4-fold risk of biliary stones (95% CI=1.1-1.9), a 1.9-fold risk of gallbladder cancer (95% CI=1.3-2.8), and a 4.8-fold risk of bile duct cancer (95% CI=2.8-8.1), compared to the reference group (third quintile: 90-124 mg/dl). Participants in the lowest quintile of high-density lipoprotein (HDL) (< 30 mg/dl) had a 4.2-fold risk of biliary stones (95% CI=3.0-6.0), an 11.6-fold risk of gallbladder cancer (95% CI=7.3-18.5), and a 16.8-fold risk of bile duct cancer (95% CI=9.1-30.9), relative to the reference group (third quintile: 40-49 mg/dl). In addition, total cholesterol, low-density lipoprotein (LDL) and apolipoprotein A (apo A) were inversely associated with biliary stones; whereas low levels as well as high levels of total cholesterol, LDL, apo A, and apolipoprotein B (apo B) were associated with excess risks of biliary tract cancers. Our findings support a role for serum lipids in gallstone development and biliary carcinogenesis.
serum lipid levels; gallstones; biliary tract cancer
Biliary tract cancers, encompassing tumors of the gallbladder, extrahepatic ducts, and ampulla of Vater, are relatively rare tumors with a high fatality rate. Other than a close link with gallstones, the etiology of biliary tract cancers is poorly understood. We conducted a population-based case-control study in Shanghai, China, to examine whether genetic variants in several DNA repair genes are associated with biliary tract cancers or biliary stones. Genomic DNA from 411 patients with biliary tract cancers (237 gallbladder, 127 bile duct, and 47 ampulla of Vater), 891 patients with biliary stones, and 786 healthy subjects randomly selected from the Shanghai population, was genotyped for 6 single nucleotide polymorphisms (SNPs) in 4 DNA repair genes (MGMT, RAD23B, CCNH, and XRCC3). Of the 6 SNPs, only one (MGMT EX5-25C>T, rs12917) was associated with biliary tract cancer. Independent of gallstones, subjects carrying the CT genotype of the MGMT EX5-25C>T marker had a significantly reduced risk of gallbladder cancer (odds ratio (OR)=0.63; 95% confidence interval (CI): 0.41-0.97; Ptrend = 0.02) and non-significant reduced risks of bile duct (OR=0.61; 95% CI: 0.35-1.06) and ampulla of Vater (OR=0.85; 95% CI: 0.39-1.87) cancers. However, this marker was not associated with biliary stones, and the other markers examined were not significantly associated with either biliary tract cancers or stones. Findings from this population-based study in Shanghai suggest that MGMT gene variants may alter susceptibility to biliary tract cancer, particularly gallbladder cancer. Confirmation in future studies, however, is required.
Biliary tract cancers; gallbladder; extrahepatic bile duct; ampulla of Vater; DNA repair; polymorphism; China
Biliary tract cancers, encompassing gallbladder, extrahepatic bile duct and ampulla of Vater cancers, are uncommon but often fatal malignancies. Hormone-related factors, including parity, oral contraceptive use, obesity, and gallstones, have been implicated in the etiology of these cancers. To further clarify the role of hormones in biliary tract cancers and biliary stones, we genotyped 18 single-nucleotide polymorphisms (SNPs) in nine genes involved in steroid hormone biosynthesis, metabolism and transport in a population-based case-control study in Shanghai, China. This study included subjects who completed an interview and provided blood, which totaled 411 biliary tract cancer and 893 biliary stone patients and 786 healthy Shanghai residents. The CYP1A1 IVS1 + 606 (rs2606345) T allele was associated with gallbladder [odds ratio (OR) = 2.0, 95% confidence interval (CI), 1.3–3.0] and bile duct cancers (OR = 1.8, 95% CI = 1.1–3.1), whereas the CYP1A1 Ex7 + 131 (rs1048943) G allele was associated with ampulla of Vater cancer (OR = 2.9, 95% CI = 1.5–5.4). After taking into account multiple comparisons for SNPs within each gene, CYP1A1 was significantly associated with gallbladder (P = 0.004) and ampulla of Vater cancers (P = 0.01), but borderline with bile duct cancer (P = 0.06). The effect of CYP1A1 IVS1 + 606 on gallbladder cancer was more pronounced among non-obese (body mass index < 23) (OR = 3.3, 95% CI = 1.8–6.1; P interaction = 0.001). Among women taking oral contraceptives, the effect of SHBG Ex8 + 6 (rs6259) on gallbladder cancer (OR = 6.7, 95% CI = 2.2–20.5; P interaction = 0.001) and stones (OR = 2.3, 95% CI = 1.1–4.9; P-interaction = 0.05) was statistically significant. Our findings suggest that common variants in hormone-related genes contribute to the risk of biliary tract cancers and stones, possibly by modulating hormone metabolism.
Each year, the Pharmacogenetics Research Network (PGRN) holds an analysis workshop for the members of the PGRN to share new methodologies, study design approaches and to discuss real data applications. This event is closed to members of the PGRN, but the methods presented are relevant to others conducting pharmacogenomics research. This special report describes many of the novel approaches discussed at the workshop and provides a resource for investigators in the field performing pharmacogenomics data analysis. While the focus is pharmacogenomics, the methods discussed are far ranging and have relevance to all types of genetic association studies: identifying noncoding variants and tag-SNPs, haplotype analysis, multivariate techniques, quantitative trait analysis, gene–gene and gene–environment interactions, and genome-wide association studies. The goal is to introduce readers to the topics discussed at the workshop and provide a direction for future development of analysis tools and methods for analysis of pharmacogenomic data.
gene–environment interactions; gene–gene interactions; genetic determinants; haplotype analysis; pharmacogenomics; QTL analysis; tag SNPs; whole-genome association
The objective of this study was to determine whether clinical, environmental, and genetic factors can be used to develop dosing algorithms for Caucasians and African Americans that perform better than giving empirical 5 mg/day.
From April 2002 through December 2005, 259 warfarin initiators were prospectively followed until they reached maintenance dose.
The Caucasian algorithm included 11 variables (R2=0.43). This model (51% within 1 mg) performed better compared with 5 mg/day (29% within 5±1 mg). The African American algorithm included 10 variables (R2=0.28). This model predicted 37% of doses within 1 mg of the observed dose; a small improvement compared with 5 mg/day (34%). These results were similar to the results we obtained from testing other (published) algorithms.
The dosing algorithms in Caucasians explained <45% of the variability and the algorithms in African Americans performed only marginally better than giving 5 mg empirically.